Contacts of the strand formed by residues 194 - 200 (chain C) in PDB entry 3DGG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C LYS 5.5 0.2 - - - -
153C ILE* 3.5 7.1 - - - +
154C ASP* 3.0 43.3 + - - +
155C GLY 4.4 1.4 + - - -
193C ASN* 1.3 76.7 - - - +
195C TYR* 1.3 69.4 + - - +
196C THR* 5.1 5.5 + - - -
211C SER* 5.9 2.2 - - - -
212C PHE 3.5 7.9 - - - -
213C ASN* 4.0 12.8 - - - -
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.7 5.2 - - + +
135C VAL* 4.3 17.7 - - + -
151C TRP* 4.9 2.5 - + + -
152C LYS 3.6 3.1 - - - -
153C ILE* 3.9 33.2 - - + -
182C LEU* 4.5 5.2 - - + -
184C LEU* 4.2 9.7 - - + +
188C GLU 4.0 0.2 + - - -
189C TYR* 2.6 56.0 + + - -
192C HIS* 3.5 32.6 + - + +
193C ASN 4.1 4.5 - - - -
194C SER* 1.3 80.7 - - - +
196C THR* 1.3 61.4 + - - +
211C SER* 3.1 23.6 - - - -
212C PHE* 3.1 46.5 + + + -
214C ARG* 4.4 2.2 - - + -
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Residues in contact with THR 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 4.4 0.2 - - - -
150C LYS 3.9 0.5 - - - +
151C TRP* 3.3 8.9 - - - -
152C LYS* 2.7 51.1 + - + +
194C SER* 5.1 4.9 + - - -
195C TYR* 1.3 77.3 + - - +
197C CYS* 1.3 61.5 + - - +
198C GLU* 4.0 16.8 - - + +
209C VAL* 3.2 34.1 - - + -
210C LYS 3.4 8.1 - - - +
211C SER* 3.3 13.1 - - - -
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Residues in contact with CYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 4.0 10.1 - - - +
120C ILE* 4.0 17.3 - - - +
137C CYS* 2.0 53.8 - - + -
149C VAL* 5.0 4.0 - - + -
150C LYS 3.4 6.1 - - - +
151C TRP* 4.0 19.5 - - + +
196C THR* 1.3 73.1 - - - +
198C GLU* 1.3 60.9 + - - +
208C ILE 3.9 1.0 - - - +
209C VAL* 3.8 1.2 - - - -
210C LYS 3.1 30.4 + - - -
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C CYS* 6.3 0.2 - - - -
139C LEU* 5.7 1.1 - - - -
149C VAL* 3.5 6.2 - - - +
150C LYS* 2.8 60.4 + - + +
152C LYS* 3.4 27.7 - - + +
196C THR* 4.0 10.1 - - + +
197C CYS* 1.3 79.7 - - - +
199C ALA* 1.3 60.0 + - - +
200C THR 4.1 0.4 - - - -
207C PRO* 3.8 24.2 - - + +
208C ILE 3.3 5.4 - - - +
209C VAL* 4.0 22.5 - - + +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PRO* 4.3 13.5 - - + -
118C VAL* 4.1 8.7 - - + -
139C LEU* 3.8 36.5 - - + +
147C ILE* 4.7 2.7 - - + -
148C ASN 3.4 5.4 - - - +
197C CYS 4.4 0.2 + - - -
198C GLU* 1.3 73.2 - - - +
200C THR* 1.3 60.7 + - - +
207C PRO* 3.1 5.0 - - - +
208C ILE* 2.8 46.9 + - + +
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Residues in contact with THR 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 3.2 5.6 - - - +
148C ASN* 2.9 54.7 + - - +
150C LYS* 3.4 27.3 + - - +
198C GLU 4.0 0.2 + - - -
199C ALA* 1.3 72.1 - - - +
201C HIS* 1.3 66.6 + - - +
204C SER 5.9 0.2 - - - +
205C THR 5.4 7.4 - - - +
206C SER 5.9 0.4 - - - -
207C PRO* 3.8 17.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il